Final stages : problems with page numbers

Good day all. Let me start by saying that I really love Scrivener. Working with Bookbaby to get my second manuscript out to print. We have run into a problem and I am lost as to how to resolve it.

For making a 6"x9" Trade size hardback book, I needed to set my print margins to 0.31" for top and bottom and initially 0.88" for left and right. The proof returned that I needed to reset my left and right margins to the right with them ending up as 1.0" left and 0.76" right. This placed my text smack dab in the center of the ‘perfect’ zone for their print system.
However, on closer inspection, I noted that the page numbers at the bottom of each page were well inside of the “NO GO” zone and after a series of emails, it was decided to adjust the top and bottom margins as well. I set them as 0.11" top and 0.51" bottom and re-ran the manuscript and received another proof. Now my text is into the upper “NO GO” zone with plenty of clear space at the bottom. However the page numbers did not move.
I can reset the page margins to really center my text in the ‘perfect’ zone, but how do I get the page numbers to shift upwards?
Standing by… thanks in advance.
I have attached a screenshot of the bottom of page 8, showing the number still in the red zone and the top of page 9 showing the encroachment into the red zone of the content text.

Firstly it is worth mentioning that Scrivener isn’t designed for doing the kind of work you are using it for. A desktop publishing program looks more like InDesign or Scribus (which is free), whereas this is a writing tool meant primarily for hashing out first drafts.

That aside, this earlier post may help